Libraries of complexes comprising an encoded molecule as well as the template which has coded for the synthesis thereof are useful in finding new chemical compounds which may be used for therapeutic purposes, because the potential drug is connected to an identifier molecule or template, which may be decoded for identification of each chemical entity that has participated in the synthetic history.
Some attempts to form the complex comprising an encoded molecule as well as the template that codes for the chemical entity that has participated in the formation of the encoded molecule, were based on the split-and-mix principle known from combinatorial chemistry, see e.g. WO 93/06121 A1, EP 643 778 B1, and WO 00/23458. If several selection rounds are desirable or necessary the split-and-mix principle has the inherent disadvantage of requiring decoding between each selection round. The decoding step may be laborious and cumbersome because the templates usually are incorporated into a vector and then subsequently into a suitable host micro organism.
Other attempts have focussed on the formation of encoded proteins using the natural machinery of a cell and connecting the formed protein with the template nucleic acid that has coded for the amino acid components of the protein. Examples of suitable systems are phage display, E. coli display, ribosome display (WO 93/03172), and protein-mRNA-fusions (WO 98/31700). The genetic information of the nucleic acid, usually mRNA or DNA, may not necessarily be decoded between each round of selection to establish the identity of the chemical entities that has formed the protein because the nucleic acid can be amplified by known means, such as PCR, and processed for the formation of a new library enriched in respect of suitable binding proteins.
Recently, new a method for encoding molecules has been suggested, which can be performed in several selection rounds without intermediate decoding, wherein the en-coded molecule is not restricted to peptides and proteins. WO 02/00419 and WO 02/103008 disclose methods for preparing virtually any molecule connected to a template coding for chemical entities which have reacted to form the molecule. In short, a template segregated into a plurality of codons and a plurality of building blocks comprising a transferable chemical entity and an anticodon are initially provided. Under hybridisation conditions, the template and building blocks are annealed together and the chemical entities are subsequently reacted to form the molecule. The methods of the prior art are, however, restricted to reactions of the chemical entities which can be performed under hybridisation conditions. Hybridisation conditions generally imply aqueous solvents, moderate pH, and ambient temperature.
WO 02/074929 and WO 04/016767 disclose template directed synthesis methods in which the reactive units of functional groups are reacted while hybridised to a template. This severely restricts the applicability of these prior art methods.